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- PDB-1ee1: CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ee1 | ||||||
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Title | CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH ONE MOLECULE ATP, TWO MOLECULES DEAMIDO-NAD+ AND ONE MG2+ ION | ||||||
![]() | NH(3)-DEPENDENT NAD(+) SYNTHETASE | ||||||
![]() | LIGASE / LYASE / AMIDOTRANSFERASE / NH3 DEPENDENT / ATP PYROPHOSPHATASE | ||||||
Function / homology | ![]() NAD+ synthase / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / glutaminase activity / NAD biosynthetic process / sporulation resulting in formation of a cellular spore / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Devedjiev, Y. / Symersky, J. / Singh, R. / Jedrzejas, M. / Brouillette, C. / Brouillette, W. / Muccio, D. / Chattopadhyay, D. / Delucas, L. | ||||||
![]() | ![]() Title: Stabilization of active-site loops in NH3-dependent NAD+ synthetase from Bacillus subtilis. Authors: Devedjiev, Y. / Symersky, J. / Singh, R. / Jedrzejas, M. / Brouillette, C. / Brouillette, W. / Muccio, D. / Chattopadhyay, D. / DeLucas, L. #1: ![]() Title: Asymmetric Complex of NAD+ Synthetase with Natural Substrates ATP Deamido-NAD+ Authors: Devedjiev, Y. / Singh, R. / Brouillette, C. / Muccio, D. / Brouillette, W. / DeLucas, L. / Jedzejas, M. #2: ![]() Title: Catalytic Cycle of NAD+ Synthetase Viewed by X-Ray Structures of Kinetic Intermediates Authors: Devedjiev, Y. / Singh, R. / Brouillette, C. / Muccio, D. / Brouillette, W. / DeLucas, L. / Jedzejas, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.9 KB | Display | ![]() |
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PDB format | ![]() | 97.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 27.5 KB | Display | |
Data in CIF | ![]() | 38.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30303.994 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P08164, NAD+ synthase (glutamine-hydrolysing) #2: Chemical | ChemComp-MG / | #3: Chemical | #4: Chemical | ChemComp-ATP / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.42 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5.2 Details: PEG400, sodium acetate, magnesium chloride, adenosine triphosphate, deamido-NAD+, pH 5.2, VAPOR DIFFUSION, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 20, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→20 Å / Num. all: 98810 / Num. obs: 33464 / % possible obs: 95.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.06→2.13 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.156 / Num. unique all: 2584 / % possible all: 82.6 |
Reflection | *PLUS Num. obs: 30068 / % possible obs: 95.4 % / Num. measured all: 136657 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 83 % / Mean I/σ(I) obs: 7.8 |
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Processing
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Refinement | Resolution: 2.06→6 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber Details: Used weighted least squares procedure. ALL PORTIONS OF THE BACKBONE IN SUBUNIT A ARE WELL ORDERED. HOWEVER, BACKBONE ATOMS AND THE SIDE CHAINS OF RESIDUES 83-86 AND 205-225 IN SUBUNIT B ARE ...Details: Used weighted least squares procedure. ALL PORTIONS OF THE BACKBONE IN SUBUNIT A ARE WELL ORDERED. HOWEVER, BACKBONE ATOMS AND THE SIDE CHAINS OF RESIDUES 83-86 AND 205-225 IN SUBUNIT B ARE NOT VISIBLE ON THE ELECTRON DENSITY MAP. THE NICOTINIC ACID MOIETY OF DEAMIDO-NAD BOUND TO SUBUNIT B IS DISORDERED AS WELL, THOUGH THE REMAINDER OF THE SUBSTRATE IS WELL ORDERED. COORDINATES OF THE NICOTINIC ACID MOIETY IN SUBUNIT B ARE PRESENTED FOR REFERENCE. ATP BINDING SITE IN SUBUNIT A IS FULLY OCCUPIED, HOWEVER, NO BINDING OF ATP AND MG2+ WAS FOUND IN SUBUNIT B.
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Refinement step | Cycle: LAST / Resolution: 2.06→6 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 6 Å / Num. reflection obs: 29684 / σ(F): 1 / Rfactor obs: 0.158 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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